FMODB ID: 3979L
Calculation Name: 3JTG-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3JTG
Chain ID: A
UniProt ID: Q3UPW2
Base Structure: X-ray
Registration Date: 2023-06-22
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptAll |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 2.20220422 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 95 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -798444.803018 |
---|---|
FMO2-HF: Nuclear repulsion | 758116.220844 |
FMO2-HF: Total energy | -40328.582174 |
FMO2-MP2: Total energy | -40447.260045 |
3D Structure
Ligand structure
Ligand Interaction
Ligand binding energy
"IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(A:272:GLY)
Summations of interaction energy for
fragment #1(A:272:GLY)
IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
-2.661 | 1.45 | 5.467 | -5.286 | -4.291 | -0.033 |
Interaction energy analysis for fragmet #1(A:272:GLY)
frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3 | A | 274 | HIS | 0 | -0.016 | -0.006 | 3.789 | -0.112 | 1.414 | -0.010 | -0.849 | -0.666 | 0.002 |
4 | A | 275 | LEU | 0 | 0.005 | -0.001 | 5.355 | -0.498 | -0.498 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 276 | TRP | 0 | 0.052 | 0.000 | 6.943 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 277 | GLU | -1 | -0.797 | -0.884 | 2.358 | -2.349 | -0.904 | 5.117 | -3.789 | -2.773 | -0.031 |
7 | A | 278 | PHE | 0 | 0.025 | 0.005 | 4.440 | -0.156 | -0.056 | -0.001 | -0.013 | -0.085 | 0.000 |
8 | A | 279 | ILE | 0 | -0.031 | -0.026 | 5.725 | 0.290 | 0.290 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 280 | ARG | 1 | 0.812 | 0.870 | 2.483 | -0.116 | 0.419 | 0.352 | -0.431 | -0.457 | -0.003 |
10 | A | 281 | ASP | -1 | -0.839 | -0.898 | 3.636 | -2.586 | -2.081 | 0.009 | -0.204 | -0.310 | -0.001 |
11 | A | 282 | ILE | 0 | 0.001 | -0.011 | 7.092 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 283 | LEU | 0 | -0.052 | -0.020 | 10.273 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 284 | ILE | 0 | -0.034 | -0.008 | 7.968 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 285 | HIS | 1 | 0.833 | 0.912 | 8.730 | 0.564 | 0.564 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 286 | PRO | 0 | 0.027 | 0.010 | 12.644 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 287 | GLU | -1 | -0.789 | -0.883 | 13.666 | -0.309 | -0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 288 | LEU | 0 | -0.028 | -0.012 | 11.276 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 289 | ASN | 0 | -0.078 | -0.030 | 14.346 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 290 | GLU | -1 | -0.781 | -0.872 | 15.747 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 291 | GLY | 0 | 0.036 | 0.020 | 18.407 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 292 | LEU | 0 | -0.029 | -0.003 | 13.943 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 293 | MET | 0 | -0.045 | -0.026 | 11.368 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 294 | LYS | 1 | 0.884 | 0.941 | 16.744 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 295 | TRP | 0 | 0.064 | 0.023 | 12.836 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 296 | GLU | -1 | -0.873 | -0.910 | 18.413 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 297 | ASN | 0 | 0.010 | -0.023 | 20.396 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 298 | ARG | 1 | 0.880 | 0.954 | 14.426 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 299 | HIS | 0 | 0.087 | 0.054 | 17.986 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 300 | GLU | -1 | -0.915 | -0.944 | 19.864 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 301 | GLY | 0 | 0.045 | 0.015 | 16.241 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 302 | VAL | 0 | -0.013 | -0.011 | 16.159 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 303 | PHE | 0 | -0.002 | -0.002 | 13.359 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 304 | LYS | 1 | 0.875 | 0.919 | 17.452 | 0.180 | 0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 305 | PHE | 0 | 0.000 | -0.006 | 14.030 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 306 | LEU | 0 | -0.034 | -0.017 | 18.262 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 307 | ARG | 1 | 0.831 | 0.893 | 19.112 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 308 | SER | 0 | 0.021 | 0.013 | 18.134 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 309 | GLU | -1 | -0.736 | -0.890 | 17.732 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 310 | ALA | 0 | 0.012 | 0.024 | 18.536 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 311 | VAL | 0 | 0.017 | 0.003 | 12.692 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 312 | ALA | 0 | -0.021 | -0.012 | 13.695 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 313 | GLN | 0 | -0.010 | -0.012 | 15.315 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 314 | LEU | 0 | 0.032 | 0.027 | 12.173 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 315 | TRP | 0 | 0.003 | 0.000 | 6.876 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 316 | GLY | 0 | 0.021 | -0.008 | 11.746 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 317 | GLN | 0 | -0.015 | -0.002 | 13.067 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 318 | LYS | 1 | 0.920 | 0.968 | 5.029 | 1.248 | 1.248 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 319 | LYS | 1 | 0.827 | 0.918 | 7.381 | 0.749 | 0.749 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 320 | LYS | 1 | 0.931 | 0.979 | 11.929 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 321 | ASN | 0 | 0.030 | 0.005 | 15.064 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 322 | SER | 0 | 0.022 | 0.001 | 17.304 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 323 | ASN | 0 | 0.031 | 0.033 | 19.560 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 324 | MET | 0 | -0.075 | -0.016 | 14.367 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 325 | THR | 0 | 0.054 | 0.020 | 18.340 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 326 | TYR | 0 | 0.007 | -0.006 | 16.918 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 327 | GLU | -1 | -0.827 | -0.881 | 18.845 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 328 | LYS | 1 | 0.916 | 0.956 | 18.421 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 329 | LEU | 0 | 0.012 | 0.020 | 12.828 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 330 | SER | 0 | -0.006 | -0.016 | 15.299 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 331 | ARG | 1 | 0.890 | 0.945 | 17.645 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 332 | ALA | 0 | -0.008 | 0.002 | 13.534 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 333 | MET | 0 | 0.002 | 0.006 | 12.667 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 334 | ARG | 1 | 0.859 | 0.904 | 15.187 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 335 | TYR | 0 | -0.004 | -0.007 | 16.151 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 336 | TYR | 0 | 0.008 | -0.003 | 9.502 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 337 | TYR | 0 | 0.041 | 0.030 | 15.285 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 338 | LYS | 1 | 0.936 | 0.975 | 18.664 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 339 | ARG | 1 | 0.943 | 0.967 | 11.127 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 340 | GLU | -1 | -0.765 | -0.856 | 16.167 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 341 | ILE | 0 | -0.024 | 0.009 | 10.646 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 342 | LEU | 0 | -0.045 | -0.025 | 12.417 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 343 | GLU | -1 | -0.804 | -0.898 | 15.380 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 344 | ARG | 1 | 0.844 | 0.923 | 18.977 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 345 | VAL | 0 | 0.028 | 0.013 | 20.573 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 346 | ASP | -1 | -0.838 | -0.934 | 23.200 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 347 | GLY | 0 | 0.004 | 0.004 | 26.336 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 348 | ARG | 1 | 0.884 | 0.943 | 24.283 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 349 | ARG | 1 | 0.999 | 0.987 | 23.832 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 350 | LEU | 0 | -0.015 | -0.010 | 20.508 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 351 | VAL | 0 | -0.015 | -0.001 | 19.585 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 352 | TYR | 0 | -0.041 | -0.028 | 16.230 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 353 | LYS | 1 | 0.917 | 0.951 | 17.131 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 354 | PHE | 0 | -0.022 | -0.004 | 9.625 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 355 | GLY | 0 | -0.001 | 0.012 | 14.448 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 356 | LYS | 1 | 0.890 | 0.934 | 14.992 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 357 | ASN | 0 | -0.066 | -0.028 | 14.250 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 358 | SER | 0 | -0.054 | -0.039 | 10.576 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 359 | SER | 0 | -0.003 | -0.008 | 9.828 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 360 | GLY | 0 | 0.045 | 0.021 | 8.691 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 361 | TRP | 0 | -0.034 | -0.028 | 9.494 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 362 | LYS | 1 | 0.857 | 0.926 | 11.760 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 363 | GLU | -1 | -0.921 | -0.988 | 15.188 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 364 | GLU | -1 | -0.921 | -0.941 | 17.717 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 365 | GLU | -1 | -0.825 | -0.896 | 12.642 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 366 | VAL | 0 | -0.029 | -0.009 | 11.204 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |